What a great resource! To keep the salamander population intact you will want to keep fish out of the pond (they will eat the salamander eggs). I wouldn't alter the current pond if you do not have to alter it. But flooding is a real issue. I am not an expert on this topic, so I have asked biologists from the Illinois Department of Natural Resources for their guidance on how you can best control flooding while still keeping the habitat you currently have in good shape. I will either e-mail you the number of one of the biologists in your area, or one of the biologists may contact you directly.